Multiple sequence alignment - TraesCS2D01G054400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G054400 chr2D 100.000 2690 0 0 1 2690 21742123 21744812 0.000000e+00 4968.0
1 TraesCS2D01G054400 chr2D 98.699 2691 30 3 1 2690 21769857 21772543 0.000000e+00 4771.0
2 TraesCS2D01G054400 chr2D 89.552 1943 115 44 654 2546 21617082 21618986 0.000000e+00 2383.0
3 TraesCS2D01G054400 chr2D 94.189 1566 62 17 880 2435 21639672 21641218 0.000000e+00 2361.0
4 TraesCS2D01G054400 chr2D 94.258 1463 63 13 953 2414 21662152 21663594 0.000000e+00 2217.0
5 TraesCS2D01G054400 chr2D 94.258 1463 63 13 953 2414 21678567 21680009 0.000000e+00 2217.0
6 TraesCS2D01G054400 chr2D 95.469 309 12 2 261 568 21659675 21659982 2.410000e-135 492.0
7 TraesCS2D01G054400 chr2D 95.146 309 13 2 261 568 21676079 21676386 1.120000e-133 486.0
8 TraesCS2D01G054400 chr2D 94.822 309 14 2 261 568 21633693 21634000 5.210000e-132 481.0
9 TraesCS2D01G054400 chr2D 93.403 288 18 1 632 918 21661861 21662148 2.480000e-115 425.0
10 TraesCS2D01G054400 chr2D 93.403 288 18 1 632 918 21678276 21678563 2.480000e-115 425.0
11 TraesCS2D01G054400 chr2D 91.005 189 17 0 632 820 21635866 21636054 3.440000e-64 255.0
12 TraesCS2D01G054400 chr2D 97.222 144 4 0 2547 2690 164771481 164771624 7.440000e-61 244.0
13 TraesCS2D01G054400 chr2D 95.918 147 6 0 2544 2690 300509007 300508861 3.460000e-59 239.0
14 TraesCS2D01G054400 chr2D 94.366 142 4 1 2412 2549 21663629 21663770 5.830000e-52 215.0
15 TraesCS2D01G054400 chr2D 94.366 142 4 1 2412 2549 21680044 21680185 5.830000e-52 215.0
16 TraesCS2D01G054400 chr2D 92.254 142 7 1 2412 2549 21641230 21641371 5.870000e-47 198.0
17 TraesCS2D01G054400 chr2D 82.648 219 33 4 43 258 103149234 103149018 3.540000e-44 189.0
18 TraesCS2D01G054400 chr2D 92.857 70 5 0 569 638 21635744 21635813 4.740000e-18 102.0
19 TraesCS2D01G054400 chr2A 90.638 1709 117 21 632 2331 23864010 23865684 0.000000e+00 2230.0
20 TraesCS2D01G054400 chr2A 94.927 887 42 1 986 1869 23826122 23827008 0.000000e+00 1386.0
21 TraesCS2D01G054400 chr2A 86.071 481 35 13 2095 2546 23827128 23827605 3.110000e-134 488.0
22 TraesCS2D01G054400 chr2A 90.415 313 21 5 632 938 23825509 23825818 1.160000e-108 403.0
23 TraesCS2D01G054400 chr2A 88.704 301 18 7 339 635 23825089 23825377 1.180000e-93 353.0
24 TraesCS2D01G054400 chr2A 88.276 290 18 6 2273 2547 23865679 23865967 1.540000e-87 333.0
25 TraesCS2D01G054400 chr2B 95.479 1305 53 5 891 2195 34867204 34865906 0.000000e+00 2078.0
26 TraesCS2D01G054400 chr2B 91.781 1387 75 13 1169 2549 34954092 34952739 0.000000e+00 1893.0
27 TraesCS2D01G054400 chr2B 94.681 376 18 2 264 638 35012294 35011920 1.390000e-162 582.0
28 TraesCS2D01G054400 chr2B 89.971 339 20 5 2225 2549 34865909 34865571 2.480000e-115 425.0
29 TraesCS2D01G054400 chr2B 92.670 191 13 1 632 821 35011888 35011698 9.490000e-70 274.0
30 TraesCS2D01G054400 chr2B 89.202 213 18 4 650 860 34867411 34867202 7.390000e-66 261.0
31 TraesCS2D01G054400 chr2B 81.517 211 34 5 1 208 368313517 368313309 4.610000e-38 169.0
32 TraesCS2D01G054400 chrUn 100.000 408 0 0 694 1101 477929041 477928634 0.000000e+00 754.0
33 TraesCS2D01G054400 chr5D 97.203 143 4 0 2548 2690 397380580 397380438 2.680000e-60 243.0
34 TraesCS2D01G054400 chr5D 97.203 143 4 0 2548 2690 536762330 536762472 2.680000e-60 243.0
35 TraesCS2D01G054400 chr5D 96.552 145 5 0 2546 2690 169481590 169481734 9.620000e-60 241.0
36 TraesCS2D01G054400 chr5D 95.333 150 6 1 2541 2690 500156420 500156568 1.240000e-58 237.0
37 TraesCS2D01G054400 chr7D 95.918 147 6 0 2544 2690 220500787 220500933 3.460000e-59 239.0
38 TraesCS2D01G054400 chr7D 82.648 219 33 4 43 258 601942070 601942286 3.540000e-44 189.0
39 TraesCS2D01G054400 chr7D 80.288 208 35 5 43 247 563541389 563541185 4.640000e-33 152.0
40 TraesCS2D01G054400 chr7D 76.587 252 50 7 19 265 555544648 555544895 2.170000e-26 130.0
41 TraesCS2D01G054400 chr5B 95.918 147 5 1 2544 2690 178555411 178555266 1.240000e-58 237.0
42 TraesCS2D01G054400 chr5B 89.583 144 10 5 108 248 521853018 521852877 7.650000e-41 178.0
43 TraesCS2D01G054400 chr6D 77.135 363 54 14 1988 2339 457592195 457591851 1.640000e-42 183.0
44 TraesCS2D01G054400 chr4D 90.071 141 9 5 108 245 509045655 509045517 7.650000e-41 178.0
45 TraesCS2D01G054400 chr1B 81.517 211 34 5 1 208 180693682 180693890 4.610000e-38 169.0
46 TraesCS2D01G054400 chr5A 89.286 56 5 1 16 70 622375929 622375874 4.810000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G054400 chr2D 21742123 21744812 2689 False 4968.000000 4968 100.000000 1 2690 1 chr2D.!!$F2 2689
1 TraesCS2D01G054400 chr2D 21769857 21772543 2686 False 4771.000000 4771 98.699000 1 2690 1 chr2D.!!$F3 2689
2 TraesCS2D01G054400 chr2D 21617082 21618986 1904 False 2383.000000 2383 89.552000 654 2546 1 chr2D.!!$F1 1892
3 TraesCS2D01G054400 chr2D 21659675 21663770 4095 False 837.250000 2217 94.374000 261 2549 4 chr2D.!!$F6 2288
4 TraesCS2D01G054400 chr2D 21676079 21680185 4106 False 835.750000 2217 94.293250 261 2549 4 chr2D.!!$F7 2288
5 TraesCS2D01G054400 chr2D 21633693 21641371 7678 False 679.400000 2361 93.025400 261 2549 5 chr2D.!!$F5 2288
6 TraesCS2D01G054400 chr2A 23864010 23865967 1957 False 1281.500000 2230 89.457000 632 2547 2 chr2A.!!$F2 1915
7 TraesCS2D01G054400 chr2A 23825089 23827605 2516 False 657.500000 1386 90.029250 339 2546 4 chr2A.!!$F1 2207
8 TraesCS2D01G054400 chr2B 34952739 34954092 1353 True 1893.000000 1893 91.781000 1169 2549 1 chr2B.!!$R1 1380
9 TraesCS2D01G054400 chr2B 34865571 34867411 1840 True 921.333333 2078 91.550667 650 2549 3 chr2B.!!$R3 1899
10 TraesCS2D01G054400 chr2B 35011698 35012294 596 True 428.000000 582 93.675500 264 821 2 chr2B.!!$R4 557


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
88 89 0.178068 GCTCTGGGAATTACAGGCGA 59.822 55.0 9.12 0.0 36.62 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 7750 8.424918 TGATACCTGAAGAGAATAGTGAATTCC 58.575 37.037 2.27 0.0 44.44 3.01 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.262950 CGTGAAGTGACGAAAATGCCA 59.737 47.619 0.00 0.00 42.10 4.92
88 89 0.178068 GCTCTGGGAATTACAGGCGA 59.822 55.000 9.12 0.00 36.62 5.54
93 94 1.507141 GGGAATTACAGGCGATGGCG 61.507 60.000 0.00 0.00 41.24 5.69
196 197 4.156008 GGTCCTAAACGCATCAAACAATCT 59.844 41.667 0.00 0.00 0.00 2.40
201 202 5.895636 AAACGCATCAAACAATCTATCCA 57.104 34.783 0.00 0.00 0.00 3.41
375 376 3.502191 TTTCTTTTTCGTGCAAGCACT 57.498 38.095 21.35 0.00 44.16 4.40
441 443 2.787473 TCAGAAATGCCCACGAGAAT 57.213 45.000 0.00 0.00 0.00 2.40
449 451 1.243902 GCCCACGAGAATTCAACCAA 58.756 50.000 8.44 0.00 0.00 3.67
1680 7516 0.905357 AGGTCGTCCATCCCTTGAAG 59.095 55.000 0.51 0.00 35.89 3.02
1795 7631 4.567537 GCTGCCATGTAATATGATGGGGTA 60.568 45.833 0.00 0.00 39.75 3.69
1910 7750 7.218773 CACGATGTTGGTTTCTTAATATTGCAG 59.781 37.037 0.00 0.00 0.00 4.41
2125 7967 9.739276 AGAGAAACACATGAAGTTTTCCATATA 57.261 29.630 17.52 0.00 39.15 0.86
2557 8501 5.864418 TCTAGTACATATGTGTTGGGGAC 57.136 43.478 18.81 6.59 39.77 4.46
2605 8549 4.993584 ACGCATCACCAAGATCAATCTATC 59.006 41.667 0.00 0.00 35.76 2.08
2610 8554 6.715347 TCACCAAGATCAATCTATCGAGAA 57.285 37.500 0.00 0.00 35.76 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 0.582005 GACGCCATCGCCTGTAATTC 59.418 55.000 0.00 0.00 39.84 2.17
88 89 3.039011 AGTATTAGAACTGGGACGCCAT 58.961 45.455 0.00 0.00 0.00 4.40
172 173 1.801771 TGTTTGATGCGTTTAGGACCG 59.198 47.619 0.00 0.00 0.00 4.79
196 197 1.672854 CCACTCTCGGCCGTTGGATA 61.673 60.000 27.15 2.82 0.00 2.59
329 330 1.823250 GCCACTTGGGAAGGACAATGT 60.823 52.381 0.00 0.00 40.01 2.71
375 376 5.163864 CGCAAGCATGACAATAGTTACTTGA 60.164 40.000 0.00 0.00 36.28 3.02
441 443 2.123589 TGTCTCTCCTGGTTGGTTGAA 58.876 47.619 0.00 0.00 37.07 2.69
449 451 0.712979 TCCCAGATGTCTCTCCTGGT 59.287 55.000 0.00 0.00 44.46 4.00
1680 7516 9.449719 TCTTCTAATTCCTGGTATCAAACTTTC 57.550 33.333 0.00 0.00 0.00 2.62
1910 7750 8.424918 TGATACCTGAAGAGAATAGTGAATTCC 58.575 37.037 2.27 0.00 44.44 3.01
2605 8549 3.125487 TCTCTCTCGTTGCTAGTTTCTCG 59.875 47.826 0.00 0.00 0.00 4.04
2610 8554 2.096248 CCCTCTCTCTCGTTGCTAGTT 58.904 52.381 0.00 0.00 0.00 2.24



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.